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Objective To investigate the clinical, imaging and pathological characteristics of one case of mitochondrial encephalopathy. Methods The data of physical examination, electromyopraphy (EMG), cranial CT and MRI, electroencephalography (EEG), serologic examination, and light microscopy and electron microscopy of muscle biopsy specimens of one case of mitochondrial encephalopathy were collected. The related literatures were reviewed. Results A 52-year-old female patient was admitted with an 8-month of seizures, numbness of the limbs for three times. The clinical manifestations were mainly focal seizures with intelligence disturbance and positive bilateral pyramidal tract sign. The imaging examination was considered to be ischemic stroke and cerebral atrophy. EEG revealed moderate and severe abmormal brain wave. In cerebrospinal fluid (CSF) examination, the intracranial pressure (ICP) was initially 2.01 kPa and finally 1.03 kPa, red blood cell count 1.04 × 10 6/L, white blood cell count 5 × 106/L (with an increase in neutrophilic granulocyte proportion), protein 0.70 g/L, chlorides 103.30 mmol/L and IgG 51.90 mg/L. Serum high -sensitivity C -reactive protein (hsCRP) was 15.40 mg/L, and erythrocyte sedimentation rate (ESR) 23 mm/h. Brain biopsy revealed cortical neuron swelling, loss of natural conical shape. The number of capillary increased and astrocytes proliferated reactively. Immunohistochemical examination showed that there were positive Mito granular materials inside the swelling and normal cytoplasm of neurons. The proliferative astrocytes were positive for glial fibrillany acid protein (GFAP). The electronic microscopic examination revealed that a large number of abnormal mitochondria various in shape and size were accumulated between subsarcolemma and myofibrilla. The mitochondrial cristae were flattened or prolonged and twining in concentricity. Osmiophilic bodies and crystalloid inclusion bodies were found in mitochondria. Conclusion Mitochondrial encephalopathy is a rare disease which may be misdiagnosed as ischemic stroke. The diagnosis of mitochondrial disease must be based upon clinical manifestations and laboratory examinations including serum enzymology, biochemistry, molecular biochemistry, muscular biopsy, etc. [ABSTRACT FROM AUTHOR]